Depending on the size of the knots and what exactly is going on in your legs, they may or may not go away. Probably not, if your knots are what I'm thinking they are, as knots are the gradual accumulation of scar tissue fibers.

Meaning, your tendon is actually bigger now. Thicker. Not a problem, but the way scar tissue lays down sets you up for ongoing pain and 'injury'. It happens slowly over time.

But you can make them 'healthy' with some work.

I'm in the process of filming an Achilles Tendonitis DVD, should be out in 1-2 months. It will describe all that.